Not specific to protobufs but a lot of people/projects especially if doing MVC, push the models in the API layer all the way down the stack and they become the

Not specific to protobufs but a lot of people/projects especially if doing MVC, push the models in the API layer all the way down the stack and they become the domain, instead of having a loose coupling between the domain and serialization format. In the old days we used to have DTO's for separation but they went out of fashion.